Is DCX p.Lys202del (c.602AGA[1]) pathogenic?

DCX p.Lys202del (c.602AGA[1]) is classified Uncertain significance in DCX (ClinVar, Single submitter, 2 submitters; last evaluated 2024-10-21). Absent from gnomAD; Associated with lissencephaly type 1 due to doublecortin gene mutation.

What condition is associated with DCX p.Lys202del (c.602AGA[1])?

DCX p.Lys202del (c.602AGA[1]) is associated with lissencephaly type 1 due to doublecortin gene mutation (ClinVar).

How common is DCX p.Lys202del (c.602AGA[1]) in the general population?

DCX p.Lys202del (c.602AGA[1]) is absent from gnomAD (gnomAD).

DCX p.Lys202del

Q: How is Lissencephaly type 1 due to doublecortin gene mutation inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.602AGA[1] · rs2524835099 · VCV1691104

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

lissencephaly type 1 due to doublecortin gene mutation

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 2.1, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DCX
Protein: p.Lys202del
Coding: c.602AGA[1]
MANE Select: NM_001195553
dbSNP: rs2524835099
Type: Microsatellite
Location: chrX:111401088 (GRCh38)
Structure: AlphaFold pLDDT 67.19 · 14 PDB
Residue 202: the doublecortin 2 domain; a turn

Full DCX gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

lissencephaly type 1 due to doublecortin gene mutation — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Lissencephaly type 1 due to doublecortin gene mutation (Orphanet):

Inheritance: X-linked recessive
Onset: Adolescent, Childhood, Infancy, Neonatal

Similar variants

DCX p.Lys202Glu Uncertain significance ★ ⚠ same residue
DCX p.Tyr229fs Pathogenic ★★ same condition
DCX p.Lys202= Likely benign ★★ same residue
DCX c.809-1G>A Pathogenic/Likely pathogenic ★★ same condition
DCX p.Arg178Cys Pathogenic/Likely pathogenic ★★ same condition
DCX p.Arg186Leu Pathogenic/Likely pathogenic ★★ same condition
DCX p.Arg192Trp Pathogenic/Likely pathogenic ★★ same condition
DCX p.Arg196Cys Pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/dcx-p-lys202del (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown